flatten_roda.sh

#!/usr/bin/env sh
#
# Flattens a downloaded RODA database into the format expected by OpenFold
# Args:
#     roda_dir: 
#           The path to the database you want to flatten. E.g. "roda/pdb" 
#           or "roda/uniclust30". Note that, to save space, this script
#           will empty this directory.
#     output_dir:
#           The directory in which to construct the reformatted data

if [ "$#" -ne 2 ]; then
    echo "Usage: ./flatten_roda.sh <roda_dir> <output_dir>"
    exit 1
fi

RODA_DIR=$1
OUTPUT_DIR=$2

DATA_DIR="${OUTPUT_DIR}/data"
ALIGNMENT_DIR="${OUTPUT_DIR}/alignments"

mkdir -p "${DATA_DIR}"
mkdir -p "${ALIGNMENT_DIR}"

for chain_dir in "${RODA_DIR}"/*; do
    if [ ! -d "$chain_dir" ]; then
        continue
    fi

    chain_name=$(basename "$chain_dir")

    for subdir in "$chain_dir"/*; do
        if [ ! -d "$subdir" ]; then
            echo "$subdir is not a directory"
            continue
        fi

        if [ -z "$(ls -A "$subdir")" ]; then
            continue
        fi

        subdir_name=$(basename "$subdir")

        if [ "$subdir_name" = "pdb" ] || [ "$subdir_name" = "cif" ]; then
            mv "$subdir"/* "${DATA_DIR}/"
        else
            CHAIN_ALIGNMENT_DIR="${ALIGNMENT_DIR}/${chain_name}"
            mkdir -p "${CHAIN_ALIGNMENT_DIR}"
            mv "$subdir"/* "${CHAIN_ALIGNMENT_DIR}/"
        fi
    done
done

NO_DATA_FILES=$(find "${DATA_DIR}" -type f | wc -l)
if [ "$NO_DATA_FILES" -eq 0 ]; then
    rm -rf "${DATA_DIR}"
fi